Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
Please note that bowtie (and tophat) cannot run in parallel, that is, on multiple nodes. Submitting multi-node jobs will only waste resources. In addition you must explicitly include the '-p' option to use multiple threads on a single node.
Availability and Restrictions
The following versions of Bowtie2 are available on OSC clusters:
You can use
module spider bowtie2 to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.
Bowtie2 is available to all OSC users without restriction.
Publisher/Vendor/Repository and License Type
Ben Langmead et al., Open source
Usage on Owens
module load bowtie2. The default version will be loaded. To select a particular Bowtie2 version, use
module load bowtie2/version. For example, use
module load bowtie2/2.2.9to load Bowtie2 2.2.9.
Usage on Pitzer
module load bowtie2. The default version will be loaded.